Process ChRIS trees of DICOM data and reorder by age.
- pfdicom_agesort processes ChRIS conformant PACS pull trees and reorders
content according to an explicit <year>/<month>/<exanmple> structure.
pfdicom_agesort repacks a ChRIS-default tree of MRI/DICOM data to an explicit age-reflecting organization. The program performs a mulit-pass loop over the file tree space as defined in the [–stage <stage>] flag below.
pfdicom_agesort is dervied from pfdicom_tagExtract. Please consult the documentation for pfdicom_tagExtract for additional information.
The following dependencies are installed on your host system/python3 virtual env (they will also be automatically installed if pulled from pypi):
pfmisc (various misc modules and classes for the pf* family of objects)
pftree (create a dictionary representation of a filesystem hierarchy)
pfdicom (handle underlying DICOM file reading)
The best method of installing this script and all of its dependencies is by fetching it from PyPI
pip3 install pfdicom_agesort
-I|--inputDir <inputDir> Input DICOM directory to examine. By default, the first file in this directory is examined for its tag information. There is an implicit assumption that each <inputDir> contains a single DICOM series. [-e|--extension <DICOMextension>] An optional extension to filter the DICOM files of interest from the <inputDir>. -O|--outputDir <outputDir> The output root directory that will contain a tree structure identical to the input directory, and each "leaf" node will contain the analysis results. In the case of `pfdicom_agesort`, this <outputDir> is the root of the age sorted tree. [--outputLeafDir <outputLeafDirFormat>] If specified, will apply the <outputLeafDirFormat> to the output directories containing data. This is useful to blanket describe final output directories with some descriptive text, such as 'anon' or 'preview'. This is a formatting spec, so --outputLeafDir 'preview-%s' where %s is the original leaf directory node, will prefix each final directory containing output with the text 'preview-' which can be useful in describing some features of the output set. [-F|--tagFile <tagFile>] Read the tags, one-per-line in <tagFile>, and print the corresponding tag information in the DICOM <inputFile>. [-T|--tagList <tagList>] Read the list of comma-separated tags in <tagList>, and print the corresponding tag information parsed from the DICOM <inputFile>. [-S|--symlinkDCMdata] If true/specified, perform a symlink of the original DICOM data to the final output directory tree. If false, a copy of the original DICOM data is performed. [-D|--doNotCleanUp] If true, do not cleanup the original tag data tree created when analysing the original DICOM tree structure. [-m|--image <[<index>:]imageFile>] If specified, also convert the <inputFile> to <imageFile>. If the name is preceded by an index and colon, then convert this indexed file in the particular <inputDir>. [-s|--imageScale <factor>[:<interpolation>]] If an image conversion is specified, this flag will scale the image by <factor> and use an interpolation <order>. This is useful in increasing the size of images for the html output. Note that certain interpolation choices can result in a significant slowdown! interpolation order: 'none', 'nearest', 'bilinear', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermite', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos' -o|--outputFileStem <outputFileStem> The output file stem to store data. This should *not* have a file extension, or rather, any "." in the name are considered part of the stem and are *not* considered extensions. [-t|--outputFileType <outputFileType>] A comma specified list of output types. These can be: o <type> <ext> <desc> o raw -raw.txt the raw internal dcm structure to string o json .json a json representation o html .html an html representation with optional image o dict -dict.txt a python dictionary o col -col.txt a two-column text representation (tab sep) o csv .csv a csv representation Note that if not specified, a default type of 'raw' is assigned. [--stage <stage>] Stage to execute -- mostly for debugging purposes and useful if running a particular stage repeatedly. [--infoJSON <infoJSONfile>] The name of the study JSON file. Defaults to 'info.json'. [--threads <numThreads>] If specified, break the innermost analysis loop into <numThreads> threads. [-x|--man] Show full help. [-y|--synopsis] Show brief help. [--json] If specified, output a JSON dump of final return. [--followLinks] If specified, follow symbolic links. [-v|--verbosity <level>] Set the app verbosity level. 0: No internal output; 1: Run start / stop output notification; 2: As with level '1' but with simpleProgress bar in 'pftree'; 3: As with level '2' but with list of input dirs/files in 'pftree'; 5: As with level '3' but with explicit file logging for - read - analyze - write
Process a ChRIS tree containing DICOM:
pfdicom_agesort \\ -I /neuro/users/chris/data/mrn \\ -O /neuro/users/chris/data/age \\ --threads 0 --printElapsedTime \\ -e dcm \\ -o '%_md5|6_PatientID-%PatientAge' \\ -m 'm:%_nospc|-_ProtocolName.jpg' \\ -s 3:none \\ --useIndexhtml \\ -t raw,json,html,dict,col,csv \\ --followLinks \\ --symlinkDCMdata \\ -v 3 \\ --threads 0
which will reorganize the file trees as shown, printing the final elapsed processing time.
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